Hi
This is my first post; be gentle with me. I have been using Slicer for a few years to segment CT or MRI scans and extract STL files for use with other CAE tools. I don’t use it extensively, but I have used the process that is currently giving me issues many times.
A client has provided a CT scan to me which reads in without problems, segments fine, but Slicer crashes when I try to write a STL file of the segment.
The scan is 2081 x 2081 x 1995 . The volumes output is attached.
Note the Image spacing is not correct, in x and y the spacing is 600nm and in z it is 600 um.
I segment between 12 and 254 and then try to write that to a STL file, which is when Slicer crashes. Attached is an image of memory usage at the point Slicer crashes.
Below is the output from Help>Report a bug
I presume this is a memory error, but I have more RAM that the 10X scan resolution. However, I have taken just the first 500 layers of the scan, and Slicer does not crash in this case.
I have tried the same process on the nightly build - 4.13.0-2021-05-19 - which tells me to increase the virtual memory, but then tells me there are memory leaks (I can provide this output if required).
Thanks for any help in advance.
Regards,
Mike
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Session start time …: 2021-05-22 11:19:30
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Slicer version …: 4.11.20210226 (revision 29738 / 7a593c8) win-amd64 - installed release
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Operating system …: Windows / Professional / (Build 19041, Code Page 65001) - 64-bit
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Memory …: 262065 MB physical, 366513 MB virtual
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - CPU …: GenuineIntel , 56 cores, 56 logical processors
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Qt configuration …: version 5.15.1, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Developer mode enabled …: no
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Prefer executable CLI …: yes
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Application path …: C:/Users/mike.lewis/AppData/Local/NA-MIC/Slicer 4.11.20210226/bin
[DEBUG][Qt] 22.05.2021 11:19:30 (unknown:0) - Additional module paths …: (none)
[DEBUG][Python] 22.05.2021 11:19:35 [Python] (C:\Users\mike.lewis\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Python\Lib\site-packages\pydicom\datadict.py:432) - Reversing DICOM dictionary so can look up tag from a keyword…
[DEBUG][Python] 22.05.2021 11:19:40 [Python] (C:\Users\mike.lewis\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Python] 22.05.2021 11:19:41 [Python] (C:\Users\mike.lewis\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 22.05.2021 11:19:41 [Python] (C:\Users\mike.lewis\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 22.05.2021 11:19:41 (unknown:0) - Switch to module: “Welcome”
[ERROR][VTK] 22.05.2021 11:23:45 [vtkITKArchetypeDiffusionTensorImageReaderFile (0000025137F1B380)] (D:\D\S\Slicer-1\Libs\vtkITK\vtkITKArchetypeDiffusionTensorImageReaderFile.cxx:166) - There is more than one file, use the vtkITKArchetypeImageSeriesReader instead
[INFO][VTK] 22.05.2021 11:25:12 [vtkMRMLVolumeArchetypeStorageNode (000002514BD122C0)] (D:\D\S\Slicer-1\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:509) - Loaded volume from file: D:/Dropbox/Exchange/BioMedical/OxfordBioMedical/VOI_diameter_1,3mm/meniscotot_ir_rec_voi__cor_voi_00001032.bmp. Dimensions: 2081x2081x1995. Number of components: 3. Pixel type: unsigned char.
[DEBUG][Qt] 22.05.2021 11:25:12 (unknown:0) - “Volume” Reader has successfully read the file “D:/Dropbox/Exchange/BioMedical/OxfordBioMedical/VOI_diameter_1,3mm/meniscotot_ir_rec_voi__cor_voi_00001032.bmp” “[95.82s]”
[DEBUG][Qt] 22.05.2021 11:25:51 (unknown:0) - Switch to module: “Volumes”
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[WARNING][Qt] 22.05.2021 11:25:51 (unknown:0) - Assertion this->Table->rowHeight(i) == newHeight
failed in D:\D\S\Slicer-1-build\CTK\Libs\Widgets\ctkMatrixWidget.cpp line 253
[DEBUG][Qt] 22.05.2021 11:31:14 (unknown:0) - Switch to module: “SegmentEditor”
[DEBUG][Qt] 22.05.2021 11:32:54 (unknown:0) - Switch to module: “Segmentations”